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CHANGELOG
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Glossary:
OpenMS - Name of the project and our C++ library
TOPP - "The OpenMS Proteomics Pipeline", collection of chainable tools for flexible HPLC/MS workflows
TOPPAS - "The OpenMS Proteomics Pipeline Assistant", graphical tool to interactively build and run HPLC/MS workflows
TOPPView - Versatile viewer for HPLC/MS data
INI file - parameter configuration file, holding custom parameter settings for TOPP tools
INIFileEditor - graphical parameter editor for INI files
Parameters - list of algorithm or TOPP tool parameters that changed in this release
------------------------------------------------------------------------------------------
---- OpenMS 2.0 ----
------------------------------------------------------------------------------------------
Release date: February 2015
OpenMS 2.0 is the first release after the switch to git and a complete overhaul of the
build system. It introduces a considerable number of new features and bug fixes.
Furthermore, we removed the dependency to GSL and replaced the functionality using
Eigen3 and Wildmagic. Thus, the OpenMS core and the full build are now under a more
permissive non-GPL (e.g., Apache or BSD) license.
File formats:
- mzQuantML support (experimental)
- mzIdentML support (experimental)
- mzTab support (experimental)
- Indexed mzML support
- Support for numpress encoding in mzML
- Major speed improvement in mzML / mzXML parsing (up to 4x for some setups)
TOPPView:
- Support for visualizing mass fingerprinting hits from featureXML along with their raw spectra in MS1
- Improved "Tools" -> "Goto" dialog
- Improved display of m/z, RT, and intensity values 1D and 2D view
New tools:
- FeatureFinderIdentification -- Detects features in MS1 data based on peptide identifications (TOPP)
- FeatureFinderMultiplex -- Determination of peak ratios in LC-MS data (TOPP)
- FidoAdapter -- Runs the protein inference engine Fido (TOPP)
- LowMemPeakPickerHiRes -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
- LowMemPeakPickerHiRes_RandomAccess -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
- MRMTransitionGroupPicker (UTIL)
- MSGFPlusAdapter -- MS/MS database search using MS-GF+ (TOPP)
- MetaboliteSpectralMatcher -- Find potential HMDB ids within the given mass error window (UTIL)
- OpenSwathWorkflow -- Complete workflow to run OpenSWATH (UTIL)
- PeakPickerIterative -- Finds mass spectrometric peaks in profile mass spectra (UTIL)
- RTAnnotator -- Annotates identification files that are missing the RT field (UTIL)
- SimpleSearchEngine -- Annotates MS/MS spectra using SimpleSearchEngine (UTIL)
- TopPerc -- Facilitate input to Percolator and reintegrate (UTIL)
Deprecated tools:
- DBExporter -- Exports data from an OpenMS database to a file (TOPP)
- DBImporter -- Imports data to an OpenMS database (TOPP)
- FeatureFinderRaw -- Determination of peak ratios in LC-MS data (TOPP)
- SILACAnalyzer -- Determination of peak ratios in LC-MS data (TOPP)
Status changes:
- PhosphoScoring (UTIL -> TOPP)
Tools with major changes:
- OpenSWATH now supports MS1 extraction and labelled workflows
- OpenSWATHWorkflow single binary (high performance integrated workflow)
- IsobaricAnalyzer now supports TMT 10-plex
General:
- Removed GSL dependencies
- Introduced low memory versions of various algorithms
- OpenMS now offers a single interface for different implementations to access mass spectrometric data
- in memory
- on disk with index
- cached on disc for fast access
as well as a chainable, low memory sequential processor of MS data (using a separate interface)
- pyOpenMS now supports python 3.x
- Refactored AASequence, major speed improvement (~40x) for construction of unmodified sequences
Third party software:
- Added Fido support
- Added MS-GF+ support
Changes to the Build System / Package System:
- Restructured repository layout and build system
- Added support for Travis CI
- Simplified pyOpenMS build system
- Support for Visual Studio 2013
Changed parameters:
Tool name Added/removed Parameter name Type Default value Restrictions Supported formats
AccurateMassSearch + algorithm:ionization_mode string positive positive,negative,auto
AccurateMassSearch + algorithm:keep_unidentified_masses string false false,true
AccurateMassSearch + db:mapping input-file CHEMISTRY/HMDBMappingFile.tsv *.tsv
AccurateMassSearch + db:struct input-file CHEMISTRY/HMDB2StructMapping.tsv *.tsv
AccurateMassSearch + force string false true,false
AccurateMassSearch + negative_adducts_file input-file CHEMISTRY/NegativeAdducts.tsv *.tsv
AccurateMassSearch + out_annotation output-file *.featureXML,*.consensusXML
AccurateMassSearch + positive_adducts_file input-file CHEMISTRY/PositiveAdducts.tsv *.tsv
AccurateMassSearch - algorithm:ionization_mode string positive positive,negative
AccurateMassSearch - algorithm:negative_adducts_file string
AccurateMassSearch - algorithm:positive_adducts_file string
AdditiveSeries + force string false true,false
BaselineFilter + force string false true,false
CVInspector + force string false true,false
CompNovo + force string false true,false
CompNovoCID + force string false true,false
ConsensusID + force string false true,false
ConsensusMapNormalizer + force string false true,false
ConvertTSVToTraML + algorithm:override_group_label_check string false true,false
ConvertTSVToTraML + algorithm:retentionTimeInterpretation string iRT iRT,seconds,minutes
ConvertTSVToTraML + force string false true,false
ConvertTSVToTraML + in input-file *.tsv,*.csv,*.mrm
ConvertTSVToTraML + in_type string tsv,csv,mrm
ConvertTSVToTraML - in input-file *.csv
ConvertTraMLToTSV + force string false true,false
DTAExtractor + force string false true,false
DeMeanderize + force string false true,false
Decharger + force string false true,false
DecoyDatabase + force string false true,false
Digestor + force string false true,false
DigestorMotif + force string false true,false
EICExtractor + auto_rt:FHWM double 5
EICExtractor + auto_rt:SNThreshold double 5
EICExtractor + auto_rt:enabled string false true,false
EICExtractor + auto_rt:out_debug_TIC output-file *.mzML
EICExtractor + force string false true,false
EICExtractor + in_header input-file *.txt
EICExtractor + out output-file *.csv
EICExtractor + out_separator string ,
EICExtractor - out output-file *.txt
EICExtractor - out_detail output-file *.txt
ERPairFinder + force string false true,false
ExecutePipeline + force string false true,false
FFEval + force string false true,false
FalseDiscoveryRate + force string false true,false
FeatureFinderCentroided + force string false true,false
FeatureFinderCentroided + out_mzq output-file *.mzq
FeatureFinderCentroided - algorithm:fit:epsilon_abs double 0.0001 0:
FeatureFinderCentroided - algorithm:fit:epsilon_rel double 0.0001 0:
FeatureFinderIsotopeWavelet + force string false true,false
FeatureFinderMRM + force string false true,false
FeatureFinderMetabo + algorithm:epd:enabled string true true,false
FeatureFinderMetabo + force string false true,false
FeatureFinderSuperHirn + force string false true,false
FeatureLinkerLabeled + force string false true,false
FeatureLinkerUnlabeled + force string false true,false
FeatureLinkerUnlabeledQT + force string false true,false
FileConverter + MGF_compact string false true,false
FileConverter + UID_postprocessing string ensure none,ensure,reassign
FileConverter + force string false true,false
FileConverter + out output-file *.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta,*.csv
FileConverter + out_type string mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta,csv
FileConverter + process_lowmemory string false true,false
FileConverter + write_mzML_index string false true,false
FileConverter - out output-file *.mzData,*.mzXML,*.mzML,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.edta
FileConverter - out_type string mzData,mzXML,mzML,dta2d,mgf,featureXML,consensusXML,edta
FileFilter + force string false true,false
FileFilter + peak_options:indexed_file string false true,false
FileFilter + peak_options:numpress:intensity string none none,linear,pic,slof
FileFilter + peak_options:numpress:intensity_error double 0.0001
FileFilter + peak_options:numpress:masstime string none none,linear,pic,slof
FileFilter + peak_options:numpress:masstime_error double 0.0001
FileFilter + spectra:select_polarity string unknown,positive,negative
FileInfo + force string false true,false
FileInfo + i string false true,false
FileInfo + in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid,*.mzid
FileInfo + in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid,mzid
FileInfo - in input-file *.mzData,*.mzXML,*.mzML,*.dta,*.dta2d,*.mgf,*.featureXML,*.consensusXML,*.idXML,*.pepXML,*.fid
FileInfo - in_type string mzData,mzXML,mzML,dta,dta2d,mgf,featureXML,consensusXML,idXML,pepXML,fid
FileMerger + force string false true,false
FuzzyDiff + force string false true,false
HighResPrecursorMassCorrector + force string false true,false
IDConflictResolver + force string false true,false
IDDecoyProbability + force string false true,false
IDEvaluator + force string false true,false
IDEvaluatorGUI + force string false true,false
IDExtractor + force string false true,false
IDFileConverter + force string false true,false
IDFileConverter + in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.xml,*.idXML,*.mzid
IDFileConverter + peptideprophet_analyzed string false true,false
IDFileConverter - in input-file *.pepXML,*.protXML,*.mascotXML,*.omssaXML,*.idXML
IDFilter + blacklist:ignore_modifications string false true,false
IDFilter + delete_unreferenced_peptide_hits string false true,false
IDFilter + force string false true,false
IDFilter + max_length int 0 0:
IDFilter + precursor:allow_missing string false true,false
IDFilter + precursor:mz string :
IDFilter + precursor:rt string :
IDFilter + remove_decoys string false true,false
IDFilter - max_length int 0 :0
IDMapper + consensus:annotate_ids_with_subelements string false true,false
IDMapper + force string false true,false
IDMapper + id input-file *.mzid,*.idXML
IDMapper - id input-file *.idXML
IDMassAccuracy + force string false true,false
IDMerger + add_to input-file *.idXML
IDMerger + force string false true,false
IDPosteriorErrorProbability + force string false true,false
IDPosteriorErrorProbability + out_plot output-file *.txt
IDPosteriorErrorProbability - fit_algorithm:output_name output-file
IDPosteriorErrorProbability - fit_algorithm:output_plots string false true,false
IDPosteriorErrorProbability - output_name output-file *.txt
IDRTCalibration + force string false true,false
IDRipper + force string false true,false
IDSplitter + force string false true,false
INIUpdater + force string false true,false
ITRAQAnalyzer + force string false true,false
ImageCreator + force string false true,false
InclusionExclusionListCreator + algorithm:PrecursorSelection:feature_based:max_number_precursors_per_feature int 1 1:
InclusionExclusionListCreator + algorithm:PrecursorSelection:feature_based:no_intensity_normalization string false true,false
InclusionExclusionListCreator + force string false true,false
InclusionExclusionListCreator - algorithm:PrecursorSelection:min_peak_distance double 3 0:
InclusionExclusionListCreator - algorithm:PrecursorSelection:selection_window double 2 0:
InspectAdapter + force string false true,false
InternalCalibration + force string false true,false
IsobaricAnalyzer + extraction:precursor_isotope_deviation double 10 0:
IsobaricAnalyzer + extraction:purity_interpolation string true true,false
IsobaricAnalyzer + force string false true,false
IsobaricAnalyzer + tmt10plex:channel_126_description string
IsobaricAnalyzer + tmt10plex:channel_127C_description string
IsobaricAnalyzer + tmt10plex:channel_127N_description string
IsobaricAnalyzer + tmt10plex:channel_128C_description string
IsobaricAnalyzer + tmt10plex:channel_128N_description string
IsobaricAnalyzer + tmt10plex:channel_129C_description string
IsobaricAnalyzer + tmt10plex:channel_129N_description string
IsobaricAnalyzer + tmt10plex:channel_130C_description string
IsobaricAnalyzer + tmt10plex:channel_130N_description string
IsobaricAnalyzer + tmt10plex:channel_131_description string
IsobaricAnalyzer + tmt10plex:correction_matrix string
IsobaricAnalyzer + tmt10plex:reference_channel string 126 126,127N,127C,128N,128C,129N,129C,130N,130C,131
IsobaricAnalyzer + type string itraq4plex itraq4plex,itraq8plex,tmt10plex,tmt6plex
IsobaricAnalyzer - extraction:precursor_isotope_deviation double 0.02 0:
IsobaricAnalyzer - type string itraq4plex itraq4plex,itraq8plex,tmt6plex
LabeledEval + force string false true,false
MRMMapper + force string false true,false
MRMPairFinder + force string false true,false
MSSimulator + force string false true,false
MSSimulator + in input-file *.FASTA
MSSimulator + out_id output-file *.idXML
MSSimulator - in input-file *.fasta
MapAlignerIdentification + force string false true,false
MapAlignerIdentification + model:b_spline:boundary_condition int 2 0:2
MapAlignerIdentification + model:b_spline:extrapolate string linear linear,b_spline,constant,global_linear
MapAlignerIdentification + model:b_spline:num_nodes int 5 0:
MapAlignerIdentification + model:b_spline:wavelength double 0 0:
MapAlignerIdentification - model:b_spline:break_positions string uniform uniform,quantiles
MapAlignerIdentification - model:b_spline:num_breakpoints int 5 2:
MapAlignerPoseClustering + force string false true,false
MapAlignerSpectrum + force string false true,false
MapAlignerSpectrum + model:b_spline:boundary_condition int 2 0:2
MapAlignerSpectrum + model:b_spline:extrapolate string linear linear,b_spline,constant,global_linear
MapAlignerSpectrum + model:b_spline:num_nodes int 5 0:
MapAlignerSpectrum + model:b_spline:wavelength double 0 0:
MapAlignerSpectrum - model:b_spline:break_positions string uniform uniform,quantiles
MapAlignerSpectrum - model:b_spline:num_breakpoints int 5 2:
MapAlignmentEvaluation + force string false true,false
MapNormalizer + force string false true,false
MapRTTransformer + force string false true,false
MapRTTransformer + model:b_spline:boundary_condition int 2 0:2
MapRTTransformer + model:b_spline:extrapolate string linear linear,b_spline,constant,global_linear
MapRTTransformer + model:b_spline:num_nodes int 5 0:
MapRTTransformer + model:b_spline:wavelength double 0 0:
MapRTTransformer - model:b_spline:break_positions string uniform uniform,quantiles
MapRTTransformer - model:b_spline:num_breakpoints int 5 2:
MapStatistics + force string false true,false
MascotAdapter + force string false true,false
MascotAdapterOnline + Mascot_parameters:special_modifications string Cation:Na (DE),Deamidated (NQ),Oxidation (HW),Phospho (ST),Sulfo (ST)
MascotAdapterOnline + Mascot_server:export_params string _sigthreshold=0.99&_showsubsets=1&show_same_sets=1&report=0&percolate=0&query_master=0
MascotAdapterOnline + force string false true,false
MascotAdapterOnline - Mascot_server:max_hits int 0 0:
MascotAdapterOnline - Mascot_server:query_master string false true,false
MassCalculator + force string false true,false
MassTraceExtractor + force string false true,false
MyriMatchAdapter + CleavageRules string Trypsin,Trypsin/P,Arg-C,Asp-N,Asp-N_ambic,CNBr,Chymotrypsin,Formic_acid,Lys-C,Lys-C/P,PepsinA,TrypChymo,V8-DE,V8-E,glutamyl endopeptidase,leukocyte elastase,no cleavage,proline endopeptidase,unspecific cleavage
MyriMatchAdapter + MonoisotopeAdjustmentSet string 0
MyriMatchAdapter + force string false true,false
MyriMatchAdapter - CleavageRules string Trypsin,Trypsin/P,Chymotrypsin,TrypChymo,Lys-C,Lys-C/P,Asp-N,PepsinA,CNBr,Formic_acid,NoEnzyme
MyriMatchAdapter - MonoisotopeAdjustmentSet string [-1,2]
MzTabExporter + force string false true,false
MzTabExporter + in_consensus input-file *.consensusXML
MzTabExporter + in_feature input-file *.featureXML
MzTabExporter + in_id input-file *.idXML
MzTabExporter - in input-file *.idXML
NoiseFilterGaussian + force string false true,false
NoiseFilterGaussian + processOption string inmemory inmemory,lowmemory
NoiseFilterSGolay + force string false true,false
NoiseFilterSGolay + processOption string inmemory inmemory,lowmemory
OMSSAAdapter + chunk_size int 0
OMSSAAdapter + force string false true,false
OpenSwathAnalyzer + algorithm:DIAScoring:peak_before_mono_max_ppm_diff double 20 0:
OpenSwathAnalyzer + algorithm:Scores:use_dia_scores string true true,false
OpenSwathAnalyzer + algorithm:Scores:use_ms1_correlation string false true,false
OpenSwathAnalyzer + algorithm:Scores:use_ms1_fullscan string false true,false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width double 50
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:method string legacy legacy,corrected,crawdad
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double 40
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string false false,true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 15
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 1 0:
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count int 30
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len double 1000
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:compute_peak_quality string false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:min_peak_width double -1
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:minimal_quality double -10000
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:recalculate_peaks string false
OpenSwathAnalyzer + algorithm:TransitionGroupPicker:recalculate_peaks_max_z double 1
OpenSwathAnalyzer + force string false true,false
OpenSwathAnalyzer - algorithm:EMGScoring:deltaAbsError double 0.0001
OpenSwathAnalyzer - algorithm:EMGScoring:deltaRelError double 0.0001
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:gauss_width double 50
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:peak_width double 40 0:
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:sgolay_frame_length int 15
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:sgolay_polynomial_order int 3
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:signal_to_noise double 1 0:
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:sn_bin_count int 30
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:sn_win_len double 1000
OpenSwathAnalyzer - algorithm:TransitionGroupPicker:use_gauss string true
OpenSwathAnalyzer - model:interpolation_type string cspline
OpenSwathAnalyzer - model:num_breakpoints int 5 2:
OpenSwathChromatogramExtractor + extract_MS1 string false true,false
OpenSwathChromatogramExtractor + force string false true,false
OpenSwathChromatogramExtractor + mz_window double 0.05 0:
OpenSwathChromatogramExtractor + rt_window double -1
OpenSwathChromatogramExtractor - extraction_window double 0.05 0:
OpenSwathChromatogramExtractor - model:interpolation_type string cspline
OpenSwathChromatogramExtractor - model:num_breakpoints int 5 2:
OpenSwathChromatogramExtractor - rt_extraction_window double -1
OpenSwathConfidenceScoring + force string false true,false
OpenSwathDIAPreScoring + force string false true,false
OpenSwathDecoyGenerator + enable_losses string false true,false
OpenSwathDecoyGenerator + force string false true,false
OpenSwathDecoyGenerator + mz_threshold double 0.05
OpenSwathDecoyGenerator + remove_unannotated string false true,false
OpenSwathDecoyGenerator - max_transitions int 6
OpenSwathDecoyGenerator - min_transitions int 2
OpenSwathDecoyGenerator - mz_threshold double 0.8
OpenSwathFeatureXMLToTSV + force string false true,false
OpenSwathMzMLFileCacher + force string false true,false
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_byseries_intensity_min double 300 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_byseries_ppm_diff double 10 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_centroided string false true,false
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_extraction_window double 0.05 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_nr_charges int 4 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:dia_nr_isotopes int 4 0:
OpenSwathRTNormalizer + algorithm:DIAScoring:peak_before_mono_max_ppm_diff double 20 0:
OpenSwathRTNormalizer + algorithm:EMGScoring:interpolation_step double 0.2
OpenSwathRTNormalizer + algorithm:EMGScoring:max_iteration int 500
OpenSwathRTNormalizer + algorithm:EMGScoring:statistics:mean double 1
OpenSwathRTNormalizer + algorithm:EMGScoring:statistics:variance double 1
OpenSwathRTNormalizer + algorithm:EMGScoring:tolerance_stdev_bounding_box double 3
OpenSwathRTNormalizer + algorithm:Scores:use_coelution_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_dia_scores string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_elution_model_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_intensity_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_library_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_ms1_correlation string false true,false
OpenSwathRTNormalizer + algorithm:Scores:use_ms1_fullscan string false true,false
OpenSwathRTNormalizer + algorithm:Scores:use_nr_peaks_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_rt_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_shape_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_sn_score string true true,false
OpenSwathRTNormalizer + algorithm:Scores:use_total_xic_score string true true,false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:gauss_width double 50
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:method string legacy legacy,corrected,crawdad
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:peak_width double 40
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:remove_overlapping_peaks string false false,true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_frame_length int 15
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:sgolay_polynomial_order int 3
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:signal_to_noise double 1 0:
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:sn_bin_count int 30
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:sn_win_len double 1000
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:PeakPickerMRM:use_gauss string true
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:background_subtraction string none none,smoothed,original
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:compute_peak_quality string false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:min_peak_width double -1
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:minimal_quality double -10000
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:recalculate_peaks string false
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:recalculate_peaks_max_z double 1
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:stop_after_feature int -1
OpenSwathRTNormalizer + algorithm:TransitionGroupPicker:stop_after_intensity_ratio double 0.0001
OpenSwathRTNormalizer + algorithm:add_up_spectra int 1 1:
OpenSwathRTNormalizer + algorithm:quantification_cutoff double 0 0:
OpenSwathRTNormalizer + algorithm:rt_extraction_window double -1
OpenSwathRTNormalizer + algorithm:rt_normalization_factor double 1
OpenSwathRTNormalizer + algorithm:spacing_for_spectra_resampling double 0.005 0:
OpenSwathRTNormalizer + algorithm:stop_report_after_feature int -1
OpenSwathRTNormalizer + algorithm:write_convex_hull string false true,false
OpenSwathRTNormalizer + estimateBestPeptides string false true,false
OpenSwathRTNormalizer + force string false true,false
OpenSwathRTNormalizer + outlierDetection:RANSACMaxIterations int 1000
OpenSwathRTNormalizer + outlierDetection:RANSACMaxPercentRTThreshold int 3
OpenSwathRTNormalizer + outlierDetection:RANSACSamplingSize int 10
OpenSwathRTNormalizer + outlierDetection:outlierMethod string iter_residual
OpenSwathRTNormalizer + outlierDetection:useIterativeChauvenet string false
OpenSwathRTNormalizer + peptideEstimation:InitialQualityCutoff double 0.5
OpenSwathRTNormalizer + peptideEstimation:MinBinsFilled int 8
OpenSwathRTNormalizer + peptideEstimation:MinPeptidesPerBin int 1
OpenSwathRTNormalizer + peptideEstimation:NrRTBins int 10
OpenSwathRTNormalizer + peptideEstimation:OverallQualityCutoff double 5.5
OpenSwathRewriteToFeatureXML + force string false true,false
PILISIdentification + force string false true,false
PILISModelCV + force string false true,false
PILISModelTrainer + force string false true,false
PILISSpectraGenerator + force string false true,false
PTModel + force string false true,false
PTPredict + force string false true,false
PeakPickerHiRes + algorithm:SignalToNoise:auto_max_percentile int 95 0:100
PeakPickerHiRes + algorithm:SignalToNoise:auto_max_stdev_factor double 3 0:999
PeakPickerHiRes + algorithm:SignalToNoise:auto_mode int 0 -1:1
PeakPickerHiRes + algorithm:SignalToNoise:bin_count int 30 3:
PeakPickerHiRes + algorithm:SignalToNoise:max_intensity int -1 -1:
PeakPickerHiRes + algorithm:SignalToNoise:min_required_elements int 10 1:
PeakPickerHiRes + algorithm:SignalToNoise:noise_for_empty_window double 1e+20
PeakPickerHiRes + algorithm:SignalToNoise:win_len double 200 1:
PeakPickerHiRes + algorithm:missing int 1 0:
PeakPickerHiRes + algorithm:ms_levels int 1:
PeakPickerHiRes + algorithm:spacing_difference double 1.5 0:
PeakPickerHiRes + algorithm:spacing_difference_gap double 4 0:
PeakPickerHiRes + force string false true,false
PeakPickerHiRes + processOption string inmemory inmemory,lowmemory
PeakPickerHiRes - algorithm:ms1_only string false true,false
PeakPickerWavelet + algorithm:optimization:iterations int 400 1:
PeakPickerWavelet + force string false true,false
PeakPickerWavelet - algorithm:optimization:delta_abs_error double 9.99999974737875e-05 0:
PeakPickerWavelet - algorithm:optimization:delta_rel_error double 9.99999974737875e-05 0:
PeakPickerWavelet - algorithm:optimization:iterations int 15 1:
PepNovoAdapter + force string false true,false
PeptideIndexer + IL_equivalent string false true,false
PeptideIndexer + annotate_proteins string false true,false
PeptideIndexer + force string false true,false
PeptideIndexer + write_protein_sequence string false true,false
PeptideIndexer - write_protein_sequence string false true,false
PhosphoScoring + force string false true,false
PhosphoScoring + fragment_mass_tolerance double 0.05
PhosphoScoring + fragment_mass_unit string Da Da,ppm
PhosphoScoring + out output-file *.idXML
PhosphoScoring - fragment_mass_tolerance double 0.5
PhosphoScoring - out output-file
PrecursorIonSelector + algorithm:MIPFormulation:feature_based:max_number_precursors_per_feature int 1 1:
PrecursorIonSelector + algorithm:MIPFormulation:feature_based:no_intensity_normalization string false true,false
PrecursorIonSelector + force string false true,false
PrecursorIonSelector + ids input-file *.idXML
PrecursorIonSelector - ids string
PrecursorMassCorrector + force string false true,false
ProteinInference + force string false true,false
ProteinQuantifier + average string median median,mean,weighted_mean,sum
ProteinQuantifier + force string false true,false
ProteinQuantifier + protein_groups input-file *.idXML
ProteinQuantifier - average string median median,mean,sum
ProteinQuantifier - mzTab_out output-file *.csv
ProteinQuantifier - protxml input-file *.idXML
ProteinResolver + force string false true,false
QCCalculator + force string false true,false
QCEmbedder + force string false true,false
QCExporter + force string false true,false
QCExtractor + force string false true,false
QCImporter + force string false true,false
QCMerger + force string false true,false
QCShrinker + force string false true,false
RNPxl + continue string false true,false
RNPxl + force string false true,false
RNPxlXICFilter + force string false true,false
RTEvaluation + force string false true,false
RTModel + force string false true,false
RTPredict + force string false true,false
Resampler + force string false true,false
SeedListGenerator + force string false true,false
SemanticValidator + cv input-file *.obo
SemanticValidator + force string false true,false
SemanticValidator + in input-file *.analysisXML,*.mzML,*.TraML,*.mzid,*.mzData,*.xml
SemanticValidator - in input-file *.analysisXML,*.mzML
SequenceCoverageCalculator + force string false true,false
SpecLibCreator + force string false true,false
SpecLibSearcher + compare_function string ZhangSimilarityScore PeakAlignment,SpectrumAlignmentScore,SpectrumCheapDPCorr,SpectrumPrecursorComparator,SteinScottImproveScore,ZhangSimilarityScore
SpecLibSearcher + force string false true,false
SpecLibSearcher - compare_function string ZhangSimilarityScore CompareFouriertransform,PeakAlignment,SpectrumAlignmentScore,SpectrumCheapDPCorr,SpectrumPrecursorComparator,SteinScottImproveScore,ZhangSimilarityScore
SpectraFilterBernNorm + force string false true,false
SpectraFilterMarkerMower + force string false true,false
SpectraFilterNLargest + force string false true,false
SpectraFilterNormalizer + force string false true,false
SpectraFilterParentPeakMower + force string false true,false
SpectraFilterScaler + force string false true,false
SpectraFilterSqrtMower + force string false true,false
SpectraFilterThresholdMower + force string false true,false
SpectraFilterWindowMower + force string false true,false
SpectraMerger + force string false true,false
SvmTheoreticalSpectrumGeneratorTrainer + force string false true,false
TMTAnalyzer + force string false true,false
TOFCalibration + algorithm:PeakPicker:optimization:iterations int 400 1:
TOFCalibration + force string false true,false
TOFCalibration - algorithm:PeakPicker:optimization:delta_abs_error double 9.99999974737875e-05 0:
TOFCalibration - algorithm:PeakPicker:optimization:delta_rel_error double 9.99999974737875e-05 0:
TOFCalibration - algorithm:PeakPicker:optimization:iterations int 15 1:
TextExporter + force string false true,false
TransformationEvaluation + force string false true,false
XMLValidator + force string false true,false
XMLValidator + in input-file *.mzML,*.mzData,*.featureXML,*.mzid,*.idXML,*.consensusXML,*.mzXML,*.ini,*.pepXML,*.TraML,*.xml
XMLValidator - in input-file *.mzML,*.mzData,*.featureXML,*.idXML,*.consensusXML,*.mzXML,*.ini,*.pepXML
XTandemAdapter + allow_isotope_error string yes yes,no
XTandemAdapter + force string false true,false
XTandemAdapter + output_results string all all,valid,stochastic
Resolved issues and merged pull requests:
#644 Fix header macros
#649 Fix ms numpress
#651 [INTERNAL,API] Removal of the GSL
#656 Repository layout restructuring
#657 [FIX, INTERNAL]
#658 [FIX] PeptideIndexer crashes on empty idXML (#653)
#659 [NOP] replaced c like file ending C with cpp
#660 [FIX] fix Cython 0.20 compatibility issue
#661 [BUILD,PYOPENMS] simplify pyOpenMS build system
#662 CMake and docu cleanups w.r.t. to the new layout
#664 [BUILD] build system fixes / cleanups
#665 Fix coverity errors
#666 [FEATURE] ib spectra format export
#667 [BUILD] improved handling of boost in OpenMS build system
#668 [NOP] added support for travis-ci to OpenMS
#669 [FIX] fixed AccurateMassSearch_test
#673 [FEATURE,FIX] Added min/max values to go-to dialog
#675 Checker/Test fixes and adds test for CTD writing
#677 [PYOPENMS] setup.py as minimal as possible + other improvements
#678 [FIX] fix how swath files are annotated
#679 [FIX,TEST] fixed OpenSwathDecoyGenerator / MRMDecoy
#680 [INTERNAL] Feature/CachedMzML fixes
#684 [FIX] Bugfix for threading issue in MascotGenericFile
#685 Typo fixes in documentation and licence files
#688 Fix/file size limit
#689 [FIX] disable OpenMP again for ILPDCWrapper
#690 Fix/misc
#691 further improvements to MGF::load()
#693 Major speedup of String --> Double conversion
#694 added missing index file for OMSSA test, which gets recreated when runni...
#696 [FIX] fix RAM usage when adding dataprocessing to chromatograms
#697 [FIX] proper usage of map in ControlledVocabulary
#698 Updates to FeatureFinderIdentification and the ...TraceFitter classes
#702 Feature/parallel reader
#703 Feature/aa sequence tpp
#705 [FIX] Propagate metadata in OpenSwathWorkflow
#707 [FEATURE] variable stylesheet support for qcml
#708 [BUILD] fix build system bug
#711 [FEATURE,BUILD] fix install target
#713 Fix for pepXML loading bug (#710)
#715 Feature/pyopenms wrapping improvements neu
#716 [NOP,TEST] clean up MRMDecoy, add more tests
#717 fixed 32bit memory limitation of OMSSA by chunking input data
#718 [FIX] fixed misleading warning ("Removed x peptide identifications...
#719 [CI,FIX] fix travis contrib clone problems
#721 [INTERNAL] cleanup of iostream includes
#722 Feature/mz xml consumer
#724 Feature/pyopenms mzxml consumer
#725 Fix/misc
#726 IDPosteriorErrorProbability fix
#729 Fix/coverity
#730 Feature/peak picker sn performance
#734 Feature/more pyopenms improvements
#735 [FEATURE] clang warning level
#737 [FIX] several minor fixes
#739 Feature/uids fileconverter
#741 ProteinResolver fix
#742 svn cleanup
#743 [FIX] fixed compilation error on vs2013
#747 Speedup OMSSA-XML parsing and some stats for OMSSA&XTandem
#749 Feature/python3
#750 [PYOPENMS,FIX] fixed streampos->long conversion
#751 [FEATURE] track base name when reading pep.xml files
#752 [FIX] fixed missing adaption PeptideIdentification::empty()
#754 [PYOPENMS] changed extra methods on MSSpectrum
#755 [FIX] fixed shadow warning
#756 Unity Builds
#760 [FIX-#618] fix spelling errors in headers
#761 Feature/header fixes
#764 [FEATURE] lib superhirn
#765 Feature/db removal
#768 [FIX] fixed warnings in CONCEPTS
#770 [FIX] fixed some clang warnings in stream manipulation
#771 New warnings
#773 [BUILD,PYOPENMS] fix pyOpenMS build
#775 [FIX] typos in the CMake file
#776 Fix for IDPosteriorErrorProbability on Mascot search results (#740)
#777 Memory profiling class
#779 [FIX] replaced DoubleReal and Real by double and float.
#780 [FIX] fix Swath window estimation
#781 Fix/open swath fixes
#784 [FEATURE] fix macosx pyopenms errors
#785 [FIX] VS2013 compile fixes
#786 [FEATURE] added openms_add_library function
#787 [FEATURE,BUILD] move pyOpenMS to src
#789 small fix to Win install doc for VS2013
#790 Remove "RT"; and "MZ"; metavalues from PeptideIdentification
#791 [FIX] forgot writtenDigits fixes in tests VS2013
#792 [FIX] AASequence refactoring
#794 Generic Wrapping of R scripts using GenericWrapper
#797 [NOP,DOC] removed all remaining references to FeatureFinderRaw and SILAC...
#798 Fix/py open ms testfix
#799 [DOC] removed migrated pages from doxygen. replaced by link to wiki
#800 spline interpolation of MS1 spectra
#801 RTPredict: fixed order of parameters and doc
#802 [FIX] fixed copy-paste mistake in error message
#804 [FIX] MRMDecoy: Fix neutral losses for higher charge states
#805 [PYOPENMS] added getters/setters for MZ and RT in PeptideIdentification....
#807 cubic spline implementation
#810 cubic spline interpolation
#811 [NOP] add better debug information and error handling
#812 [FIX] per cppcheck
#813 Fix/openswath
#814 [FEATURE] ConvertTSVToTraML: Support for SpectraST MRM Transition Lists
#816 Feature/cached mz ml format change
#817 [FIX] fix spline derivative for cubic spline
#819 Feature/custom i rt
#820 Fix/warnings
#821 [FIX] suppress clang warnings
#823 Feature/update numpress
#824 Fix/coverity
#826 Feature/funny pictures
#827 [FIX] fixes export macro warnings
#831 [FEATURE] fix all gcc warnings and turn warnings into errors
#832 several pyopenms fixes + updates
#833 Feature/visibility hidden
#834 Fix/fix werror
#835 Fix spline spectrum
#836 [FIX,TEST] MRMRTNormalizer_test: Windows compatibility
#838 [FIX] fixed uninitialized pointer warning
#840 [FIX] fix pyOpenMS test
#841 [BUILD] disable -Werror by default
#842 [FIX] fix dereference of iterator
#843 [FIX] fixes tests failing win debug mode
#844 [FIX] evaluation at m/z in first package now possible
#845 [FEATURE] replace String classes with StringUtils
#846 Fix/fixes from822
#847 peak boundaries and new cubic splines for PeakPickerHiRes
#850 [FEATURE] modified tests to reflect X!Tandem SLEDGEHAMMER as default
#851 Fix and tests for a bug in reading Mascot XML files
#852 [FIX] fix windows compile error
#854 [FIX] ConsensusID doesn't sort peptide hits before processing (idXML)
#855 [FIX] FalseDiscoveryRate "target+decoy"; hits should be considered as targets
#856 [FEATURE] KNIME package generation updates
#857 Fix/py open ms fix
#858 [FEATURE] ~40x speedup for constructions of unmodified AASequence
#859 Feature/SystemWildMagic
#863 [BUILD] added test for x!tandem version to enable tests only with newer ...
#865 Work-around for special modifications in Mascot (fixes #864)
#866 [FEATURE] git version embedding
#867 [FIX-#861,DOC] fixed eigen 3.2.1 problems with GammaDistributionFitter
#868 multiplex filtering
#869 [FIX] fixed problems with negative sizeof values in CachedMzML
#870 [FIX,DOC] doxygen 1.8.7 fixes
#873 [FIX] fixed macosx version query
#875 Rewrite of 'AASequence::parseString_', increasing robustness of parsing (fixes #818)
#876 [DOC] added new doc_class_only target
#880 PeakPickerHiRes peak boundaries fixed
#881 [FEATURE] mzTab 1.0
#882 [FEATURE] coding style improvements
#884 [FIX] Convert XTandem search results into .pepXML by IDFileConverter
#885 [NOP] added moc files to gitignore
#888 [FIX-#887] IDFilter errornousely removed peptidhits in multiple run files
#889 multiplex clustering
#891 [FIX] converting uniform distributed generators with normal distributions
#892 Enable loading of some pepXML files that used to cause crashes
#894 [FEATURE] improved 3rd party lib finding
#895 [FEATURE] simple search engine
#896 added scan-polarity filter to FileFilter ...
#897 (feature for Windows developers) added a small Windows .reg file
#898 More compact format for MGF files (fixes #890)
#899 [DOC] some minor documentation addition
#901 [FIX] fix MS level for DTA file reader
#902 [FIX,PYOPENMS] fix pyOpenMS after #875
#903 [FIX] mzXML fix (filterLine, basePeakMz)
#904 Feature/fix peak boundaries
#910 [FIX] fixed unity build error introduced in #845
#911 [FIX] FFCentroided replace exception handling with proper check
#914 fix index in CubicSpline2d
#916 IDMapper extension for featureMaps
#917 AccurateMassSearchEngine annotation of input map (not only mzTab output)
#919 [FIX] libc++ test fixes
#920 [FIX] fixed minor problem with knime package generation and cmake versions >2.8.11
#921 MS1 annotation in TOPPView
#922 [FIX] build system improvements
#923 EmpiricalFormula: fix (negative counts were casted away)
#924 Switch to disable tracking of Git version within OpenMS
#925 Fix/small docu improvement
#926 Feature/spellcheck
#927 PeptideIndexer: support for treating isoleucine/leucine as equivalent (resolves #872)
#928 Build System
#929 TextFile feature (skip empty lines) and docu fix
#930 check for missing peaks
#931 fix for evaluation at last node
#936 [FIX] fixed the 'variable' consumption of xslt files for a QcML file.
#938 [FEATURE] precursor scoring
#939 [FIX] fix compile error
#940 coding convention violations in MultiplexClustering fixed
#943 [FIX,PYOPENMS] fix pyOpenMS after #889
#944 [FIX,TOOLS] pyopenms parser fix
#945 [FEATURE] pyopenms wrap improved
#946 OPENMS_DLLAPI removed from GridBasedClustering
#947 [FEATURE] FeatureFinderMultiplex
#949 Fix/xml escape
#950 Feature/traml heavylight
#951 [FIX] add setOptions method for FileHandler
#955 Fix/xml escape
#958 [FIX] disallow concurrent access to the static PRNG
#959 Feature/pyopenms copyconstr
#960 [FEATURE] peptide group label new
#962 [FIX] QCCalculator now computes TIC only on MS1 spectra (fixes #96)
#964 [FIX] check for invalid charge ranges in search engine adapters (see #963)
#965 [FEATURE] tmt 10plex support
#966 [FEATURE] chaining consumer
#967 [FEATURE,TEST] mssim more ground truth in id xml
#968 [FEATURE] export PT value analogous to predicted rt value in TextExporte...
#969 [FEATURE] add a low memory FileConverter option
#970 [FEATURE] test if java can be executed
#972 Fix/file cleanup
#973 [FIX] validate presence of input file before starting executable
#977 [FEATURE] replaced pphires ms1_only flag with ms_levels parameter
#981 Feature/TextExporter_mzML
#983 [FEATURE] add library check on Windows for correct lib arch
#984 [NOP] add heavy methyl SILAC labels to unimod.xml
#985 [FEATURE] bspline support using eol bsplines implementation
#988 [FIX] simplified EmpiricalFormula
#990 [FIX,FEATURE] TransformationModelInterpolated readded
#993 Feature/sort on load (mzML, mzXML)
#994 fixes mass traces in featureXML output
#995 fixes CubicSpline2d constructor exceptions
#996 allow for SplinePackages based on just two data points
#1000 fixes problems with ">>" generated in nested C++ templates
#1001 Fix/py open ms test
#1002 [pyOPENMS] features
#1003 [FIX] fixes random fails of MSSim_test
#1006 [FEATURE] enable gui less OpenMS
#1009 update unimod.xml with newest version from unimod.org
#1010 [FIX] external code tests updated/fixed
#1011 [FIX] external project doc
#1012 [FEATURE] decreased memory footprint of Feature class by up to 44%
#1014 TOPPView: group separator for mz,rt and int values in 1D and 2D canvas
#1019 [FIX] fixed unitybuild problem on win32 with eol-bsplines
#1020 [NOP] updated copyright/license header to 2014
#1021 Feature/py open ms fixes and wraps
#1024 sorting mass shifts in FeatureFinderMultiplex
#1025 Fix/checker fixes
#1026 additional example in SplineSpectrum test
#1027 Adapter for Fido (protein inference engine), solves #808
#1029 [FIX-#184] remove public vector/map inheritance
#1032 fixes peak boundaries in PeakPickerHiRes (resolves #1022)
#1034 [FIX] improve set_peaks documentation
#1035 B-spline interpolation for peak width estimation in MultiplexClustering class
#1036 [FEATURE,API] Removed template parameter from FeatureMap
#1037 Fix/ TraML load/store
#1038 Feature/py open ms wraps
#1039 Fix/debug fix
#1040 Fix/spellcheck
#1044 [FIX:#1043]fixed featureXML reading spectrum_reference as String
#1045 [FIX] fix compile issue on win32 systems
#1046 Fix/py open ms wrap
#1047 [FIX] first probe install path, then the build path for share/OpenMS
#1048 Feature/peptide hit protein locations
#1050 Re-added B-spline transformation for non-linear RT alignment in MapAlignerIdentification
#1051 [FIX] made arguments and functions in BSpline2d const (if possible)
#1055 [FEATURE] improved purity computation for IsobaricAnalyzer
#1056 [FIX] UniqueIdGenerator susceptible to identical RNG seeds
#1057 GenericWrapper doc has minor quirks
#1058 Feature/openswathwf add
#1059 Switch to version 2.0
#1061 FeatureFinderIdentification: documentation, tests, parameter improvements
#1063 Fix/accession nr
#1065 PeakPickerHiRes docu updated
#1067 Testing/mzid
#1069 Fix and test for issue #1068 (bug in "AASequence::operator<" involving N-terminal modifications)
#1070 removing zeros in profile data caused by Thermo bug
#1072 PeakPickerHiRes: disable spacing constraints for chromatograms (fixes #1060)
#1074 'intensity weighted mean'; averaging added to ProteinQuantifier, solves #830
#1076 Adapter for MS-GF+ search engine
#1077 [TESTING] download and add MSGFPlus in travis-ci
#1078 [FEATURE] export aabefore and aaafter in peptideindexer
#1079 Linear extrapolation (and other options) for B-spline transformation
#1080 [NOP] refactored PeptideHit protein accession extraction to true member
#1082 [NOP] removed index file as these are recreated by MSGF+ anyways
#1083 Feature/mz tab fixes
#1084 [FIX] compile fixes
#1086 Update (indistinguishable) protein groups when filtering protein identifications (fixes #748)
#1087 centroided input data for FeatureFinderMultiplex
#1088 Fix FileConverter's "write_mzML_index" flag
#1089 Fix/mzid
#1090 Enable mzIdentML input in IDFileConverter
#1091 Feature/mz tab cleanup
#1092 [NOP] removed unnecessary index files
#1094 [FIX] fixed small bugs preventing a build on windows
#1097 [FIX] consistent use of wildmagic
#1098 Revert "[FIX] consistent use of wildmagic"
#1099 [FIX,BUILD] fix Windows build
#1100 Fix/windows fix
#1101 optimisation for knockout searches in FeatureFinderMultiplex
#1102 Fix/fix spellcheck
#1104 [FIX] fix compile warning from unused variables
#1108 [FIX] fix compile warnings and increase QT min version to 4.6
#1109 [FIX] removed support for multiple id formats in tools without
#1115 fix some windows compile warnings
#1116 fix segfaults in XTandemXMLFile and IsobaricChannelExtractor
#1118 Feature/swath window loader
#1121 [FIX] some VC 2013 static tests fixed
#1122 Fix PeakPicker Wavelet
#1123 [FEATURE] remove PeakType template argument from FeatureFinder
#1124 [NOP] addendum to #1123
#1125 optimisations in FeatureFinderMultiplex
#1126 [FIX] intermediate fix for win32 systems
#1127 [FEATURE] create uncrustify branch
#1128 Fix/RT meta value related bug, removed unused comment
#1131 Make BuildSystem's LibCheck fail-safe
#1135 Fix/ams mz tab export
#1136 [NOP] uncrustified
#1137 [FIX] added -b option to create new branch
#1140 [FIX] fixed bugs in AScore implementation and added deisotoping as
#1141 Fix AccurateMassSearch and visualization
#1145 Fix/spellchecks
#1147 Fix/copyright update
#1150 Added PhosphoScoring tool to TOPP documentation
#1151 Changelog 2.0
#1152 [FIX,PYOPENMS] fix and adopt pyOpenMS
#1153 minor amendmend to last fix (better console output)
#1154 [TEST] fix test
#1156 [FIX-#618] fix spelling errors
#1157 [NOP] correct version in LICENSE file
#1158 [FIX] make identifier of multiple identification runs unique
#1161 pyOpenMS 2.0 features
#1162 [FIX] fixed study variable index start at 1. Added global identifiert to
#1164 [FIX] pepXML does on some occassion contain very small fixed
#1165 Added minimal test cases for checker.php Missing test errors
#1169 [FIX] fixed segfault if searchparam requested on empty proteinids
#1170 [FIX,TEST] FidoAdapter test
#1172 [FIX] fix for the write out of mzid
#1173 [FIX] changed path String parameter to input files
#1174 [TRAVIS] added Fido executables and adapted to new directory structure
#1175 [FEATURE] add ConsensusMap push_back
#1176 [BUILD] added support for new thirdparty executables in KNIME
#1179 [FIX] added missing option to apply e-value filtering
#1180 [FIX] fix toolnames for KNIME packaging
#1181 fixed minor typo in error message
#1184 [FIX] we decided to add the missing struct mapping file and in the
#1185 [FIX] added missing elements and spike ins
#1186 Fix/docu qc mzid
#1187 [FIX] AMS: export observed-Mass in mzTab as well
#1188 [Build] Added support for new third party binaries for dmg packaging. Adapted Li...
#1189 Feature/sn
#1190 [TEST] fix test
#1192 [FIX] HMDB: removed duplicates introduced by including spike ins
#1194 [NOP] removed deprecated qc toppas workflow
#1195 [STYLE] Changed header guards mentioned by checker.php
#1196 [FIX] XTandemAdapter added option to disable isotope error flag
#1198 [TEST] fix
#1199 [TEST,FIX] changing the order of the test fixes the issue
#1201 Fix/lp wrapper param file
#1203 [TEST,FIX] set reasonable comparison tolerance
#1204 Removes debug code from FeatureFinderMultiplex
#1206 [TEST] fix test error
#1212 [FIX] and/or extension to IDFilter: Added support for old target_decoy user param in decoy filtering.
#1213 [DOC] improve linux install doc
#1215 [FIX] export AMS result as valid mzTab
#1218 [FIX] consistent use of wildmagic: TransformationModelLinear
#1219 [FIX] Map index stored as meta value in peptide identification
#1220 change parameter ranges in FeatureFinderMultiplex
#1224 updated KNIME license
#1225 [FIX][TEST] Fido replacing scores
#1226 Ammend to pull request #1212
#1228 [FIX, PYOPENMS] fixed pxd file
#1229 [DOC] merged License.txt and LICENSE for more complete description
#1230 Updated ACTIVE_MAINTAINERS with people commiting, starting in 2012. Remo...
#1231 Added Deuterium and Tritium to Elements.xml, as LIPIDMAPS contains sum f...
#1232 Fix amt
#1237 [FIX] minimum value for max_length should be 0 not -Inf
#1240 [FIX] Fix/id filter blacklist
#1242 Fix amt
#1243 fixes INIUpdater test
#1246 Updated problematic FidoAdapter test (fixes #1171)
#1247 [FIX] added missing function
#1248 [FIX, PYOPENMS] ammend to last commit
#1249 Documentation improvements (and minor fixes)
#1250 Another FidoAdapter test fix
#1253 [FIX] IsobaricAnalyzer: set charge states of consensus features
#1254 [DOC,FIX] Updated CHANGELOG, changelog_helper.sh
#1256 Fix MSGFPlusAdapter running in TOPPAS (mzid output)
#1257 Clean-up of UTILS documentation
#1261 [KNIME] adapted parameter naming for FidoAdapter in KNIME
#1262 IDFilter reports empty results
#1263 [FIX] moved TopPerc to UTILS and changed experimental status of MSGFPlus
#1266 [FIX] ammend to last commit
#1267 [FIX] fix conversion from Feature with Masstraces to MSExperiment
#1269 IsobaricAnalyzer: documentation, warning fix
#1270 [FIX] lexical cast is discouraged. Use of build in functions.
#1273 [FIX][BUILD] Fixes linking issue with boost in UTILS #1272
#1275 [FEATURE] [FIX] mass trace RT spacing
#1283 [PYOPENMS] Better PepXMLFile write support
#1284 [FIX] KNIME execution of MSGFPlusAdapter
#1286 [FIX] set low memory log type correctly
#1290 [FIX, PYOPENMS] fix python binding for MassTrace
#1305 [FIX] Fix/id mapper statistics
#1307 remove OS X specific code for opening folders
#1309 [FIX] Ammend to #1284
#1315 sync develop additions
------------------------------------------------------------------------------------------
---- OpenMS 1.11.1 ----
------------------------------------------------------------------------------------------
Release date: November 2013
OpenMS 1.11.1 is a bugfix release resolving the following issues with OpenMS 1.11:
TOPPAS:
- fixed bug that caused TOPPAS to crash when a connection between nodes was added under certain circumstances
TOPP:
- XMLValidator can now be used on mzML files
- fixed bug in MSSimulator/EnzymaticDigestion where amino acid "U" was leading to crash
- fixed some problems with protein modifications in MascotAdapterOnline
- fixed potential problems of TOPP help screens on small screens / small terminal windows
Build system:
- fixed issues with CMake 2.8.12
- fixed potential clang compile errors
General:
- fixed issues with MIME types in KNIME
Resolved issues:
#606 TOPPAS crashes during creation of certain edges.
#609 MascotAdapterOnline: Problems with modifications
#614 Amino acid "U" leads to crash in MSSimulator/EnzymaticDigestion
#629 OpenMS is incompatible with CMake 2.8.12
#630 Knime mime.types file should have lower case mime type names
#633 ConsoleUtils::breakString triggers uncaught exception if terminal size is too small
------------------------------------------------------------------------------------------
---- OpenMS 1.11 ----
------------------------------------------------------------------------------------------
Release date: August 2013
OpenMS 1.11 is the first release with fully integrated Python bindings (termed pyOpenMS).
For further details, please refer to https://pypi.python.org/pypi/pyopenms
File formats:
- QcML support
- pepXML exported from Mascot (added support)
- mzTab updated to 1.0RC3
- ParamXML updated to v 1.6.2
- support for CTD schema 0.3
- full support of sourceFile tag in mzML (all source files are written, SHA1 support)
TOPPView:
- handle .mzML file with mixed spectra and chromatograms (prefer spectra)
- chromatograms of all types can be displayed (not just SRM)
- link to documentation and webpage fixed
- fix a segfault when loading empty chromatograms into TOPPView
TOPPAS:
- link to documentation and webpage fixed
TOPP tools:
- MODIFIED:
- FeatureLinkerUnlabeledQT: performance (speed and memory) improvement
- FeatureLinkerUnlabeled: performance (memory) improvement (now constant in number of input maps)
- MapAlignerPoseClustering: performance (memory) improvement (now constant in number of input maps)
- EICExtractor: critical bugfix if the input map was not sorted
- PeptideIndexer: by default now demands that the peptide is fully tryptic ("-enzyme:specificity none" restores the old behavior)
- FileFilter: filter MS2 spectra by consensus map feature overlap, collision energy, isolation window width
- ProteinResolver: documentation and interface improvements
- QCCalculator/QCEmbedder/QCExtractor: multiple improvements
- WindowMower: speed improvement (movetype either slide or jump [faster])
- ADDED
- AccurateMassSearch: AccurateMassSearch assembles metabolite features from singleton mass traces.
- IsobaricAnalyzer: Extracts and normalizes isobaric labeling information from an MS experiment. This merges the previous TMTAnalyzer and ITRAQAnalyzer functionality
- QCExtractor: Extracts a table attachment to a given qc parameter
- QCImporter: Embed tables or pictures in QcML
General:
- Python bindings allow full access to the OpenMS API from Python
- TOPPTools now support passing of all parameters on the command line (use --helphelp)
- Better chromatogram support (for NoiseFilterGaussian, NoiseFilterSGolay, PeakPickerHiRes)
Search engine support:
- Mascot 2.4 is now supported
- OMSSAAdapter with improved memory footprint
- N-terminal modifications work now with X!Tandem
Changes to the Build System / Package System:
- shared linking works for all contrib packages with automated detection using CMake find modules
- upgrade of xerces to version 3.1.1
- upgrade of libsvm to version 3.12
Development:
- public inheritance from std::vector and std::set has been reduced in the
OpenMS codebase (removed from ConsensusFeature, FeatureMap, ConsensusMap,
MSExperiment)
- addition of the OpenMS/INTERFACES folder which contains proposed OpenMS
interfaces for reading/writing spectra
Deprecated:
- TMTAnalyzer, ITRAQAnalyzer -> please use IsobaricAnalyzer instead
- Several functions provided by std::vector in the MSSpectrum interface are now
deprecated (e.g. push_back, reserve etc.)
Resolved issues:
#120 Improve visual representation of edges
#151 Optimize time/memory efficiency of critical tools/algorithms